Genomic data of the American Flamingo (Phoenicopterus ruber ruber).

Dataset type: Genomic
Data released on May 20, 2014

Zhang G; Li B; Li C; Gilbert MTP; Jarvis ED; The Avian Genome Consortium ; Wang J (2014): Genomic data of the American Flamingo (Phoenicopterus ruber ruber). GigaScience Database. http://dx.doi.org/10.5524/101035

DOI10.5524/101035

The Caribbean Flamingo (Phoenicopterus ruber ruber (Linnaeus, 1758)) is a sub-species of, and commonly referred to as the American Flamingo (Phoenicopterus ruber). The Caribbean Flamingo is found generally throughout the Caribbean and is a non-migratory bird (those that do migrate only move between summer and winter breeding grounds). It is a largely social bird that breeds in huge colonies, and is a homeothermic endotherm - an animal that keeps a consistent temperature that is regulated within its body.
These data have been produced as part of the Avian Phylogenomics Project. DNA was collected from a male (leg band GWX) who had lived at the Copenhagen Zoo in Denmark, and was tended to by Mads Bertelsen. We sequenced the 1.24Gb genome to a depth of approximately 33X.
The assembled scaffolds of high quality sequences total 1.14Gb, with the contig and scaffold N50 values of 16kb and 37kb respectively. We identified 14,024 protein-coding genes with a mean length of 11.7kb.

Additional details

Read the peer-reviewed publication(s):

Zhang, G., Li, B., Li, C., Gilbert, M. T. P., Jarvis, E. D., & Wang, J. (2014). Comparative genomic data of the Avian Phylogenomics Project. GigaScience, 3(1). doi:10.1186/2047-217x-3-26
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … Meredith, R. W. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. doi:10.1126/science.1251385
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … Howard, J. T. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320–1331. doi:10.1126/science.1253451

Related datasets:

doi:10.5524/101035 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA212904
SRA: SRP029345

Projects:







Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Caribbean flamingo - TG99218American FlamingoPhoenicopterus ruber ruber Source material identifiers:Tom Gilbert
Estimated genome size:1.24
Funding source:BGI
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Caribbean flamingo - TG9Coding sequenceFASTA5.06 MB2014-02-07
Caribbean flamingo - TG9Sequence assemblyFASTA340.91 MB2014-02-07
Caribbean flamingo - TG9AnnotationGFF1.25 MB2014-02-07
Caribbean flamingo - TG9Protein sequenceFASTA3.29 MB2014-02-07
Caribbean flamingo - TG9Repeat sequenceUNKNOWN6.36 MB2014-02-07
Displaying 1-5 of 5 File(s).
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